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- PDB-4zos: 2.20 Angstrom resolution crystal structure of protein YE0340 of u... -

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Basic information

Entry
Database: PDB / ID: 4zos
Title2.20 Angstrom resolution crystal structure of protein YE0340 of unidentified function from Yersinia enterocolitica subsp. enterocolitica 8081]
Componentsprotein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Yersinia enterocolitica subsp. enterocolitica 8081 / hypothetical protein YE0340 / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHalavaty, A.S. / Wawrzak, A. / Onopriyenko, O. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.20 Angstrom resolution crystal structure of protein YE0340 of unidentified function from Yersinia enterocolitica subsp. enterocolitica 8081]
Authors: Halavaty, A.S. / Wawrzak, A. / Onopriyenko, O. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
B: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
C: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
D: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2536
Polymers49,0644
Non-polymers1902
Water1,33374
1
C: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
D: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6273
Polymers24,5322
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-26 kcal/mol
Surface area10490 Å2
MethodPISA
2
A: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
B: protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6273
Polymers24,5322
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-27 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.675, 37.135, 82.583
Angle α, β, γ (deg.)87.66, 88.25, 61.17
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERVALVALAA6 - 1019 - 104
21SERSERVALVALBB6 - 1019 - 104
12METMETSERSERAA1 - 1024 - 105
22METMETSERSERCC1 - 1024 - 105
13SERSERSERSERAA6 - 1029 - 105
23SERSERSERSERDD6 - 1029 - 105
14SERSERVALVALBB6 - 1019 - 104
24SERSERVALVALCC6 - 1019 - 104
15SERSERVALVALBB6 - 1019 - 104
25SERSERVALVALDD6 - 1019 - 104
16SERSERSERSERCC6 - 1029 - 105
26SERSERSERSERDD6 - 1029 - 105

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081


Mass: 12265.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: Yersinia enterocolitica subsp. enterocolitica 8081 / Plasmid: pMCSG7-Halo / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: A0A0M3KL35*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Crystallization: 20%Polyethylene Glycol 8000, 0.2M Sodium Chloride,Phosphate-Citrate Protein at 20 mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2015
RadiationMonochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 18325 / % possible obs: 96.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.5
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 3.2 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X7V

1x7v


Resolution: 2.2→29.66 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.888 / SU B: 7.299 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28529 931 5.1 %RANDOM
Rwork0.22883 ---
obs0.23165 17175 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.256 Å2
Baniso -1Baniso -2Baniso -3
1--18.95 Å21.75 Å212.1 Å2
2---9.65 Å2-6.08 Å2
3---28.6 Å2
Refinement stepCycle: 1 / Resolution: 2.2→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 10 74 3366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193400
X-RAY DIFFRACTIONr_bond_other_d0.0050.023193
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9794627
X-RAY DIFFRACTIONr_angle_other_deg1.18537387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5695408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.61924.535172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.59915601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1211525
X-RAY DIFFRACTIONr_chiral_restr0.1040.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213808
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02733
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A55220.13
12B55220.13
21A60540.09
22C60540.09
31A54870.13
32D54870.13
41B53920.14
42C53920.14
51B57330.09
52D57330.09
61C54210.14
62D54210.14
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 76 -
Rwork0.264 1167 -
obs--90.6 %

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